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CreateAnalysis

The hci.gnomex.httpclient.CreateAnalysisMain is a Java application that can be executed in a batch job to deposit analysis files in GNomEx. The app will create a new Analysis entry in GNomEx and return the file location where the analysis files should be deposited.

To run, you will need the following files:

  • gnomex_client.jar
  • gnomex_httpclient.properties


To get the command line usage, run:

>java -classpath gnomex_client.jar hci.gnomex.httpclient.CreateAnalysisMain
hci.gnomex.utility.CreateAnalysisMain 
   -properties <propertiesFileName>
   -server <serverName>
   -name <analysisName> 
   -lab <lab name> 
   -folderName <name of folder> 
   -organism <organism> 
   -genomeBuild <genome build> 
   -analysisType <analysis type> 
   [-debug]
   [-description <analysisDescription>]
   [-folderDescription <description of folder>]
   [-seqLane <seq lane number> [..]]

The mandatory arguments are:

  • -properties file path to the gnomex_httpclient.properties
  • -server the domain name of server that GNomEx runs on (example: bioserver.hci.utah.edu)
  • -name the name of the analysis entry
  • -lab the lab that this analysis entry belongs to (example: Brad Cairns).
  • -folderName the folder that the analysis entry should be placed in
  • -organism the species name (example: Human, E. coli)
  • -genomeBuild the genome build (example: hg19)
  • -analysisType the type of analysis (example: Alignment,SNP/INDEL,ChIP-Seq analysis)


Optional arguments are:

  • -debug turn on for more informative debugging messages
  • -description the description of the analysis entry
  • -folderDescription the description of the analysis folder
  • -idSequenceLane the ids of the sequence lanes to associate with this analysis
  • -seqLane the sequence lane number from the GNomEx experiment to associate with this analysis (to associate the raw data with the analyzed data.) This is a repeating item, so provide -seqLane argument for each sequence lane.

Here is an example:

>java -classpath gnomex_client.jar hci.gnomex.httpclient.CreateAnalysisMain 
    -name "analysis abc"
    -folderName my-analysis-folder 
    -genomeBuild hg19 
    -organism Human 
    -analysisType Alignment 
    -server bioserver.hci.utah.edu 
    -description "a description of analysis abc" 
    -properties gnomex_httpclient.properties 
    -lab "Brad Cairns"
    -seqLane 8734F1_1 -seqLane 8734F1_2

In this example created an Alignment analysis titled "analysis abc" for the Cairns lab for Human genome build hg19. We associated the analysis with 2 sequence lanes (8734F1_1 and 8734F1_2) from the original Illumina HiSeq experiment raw data.

Output from the application looks like this:

<SUCCESS idAnalysis="303" idAnalysisGroup="116"
filePath="/path/to/AnalysisData/2011/A303">